Companion diagnostics for mitochondrial inhibitors

ABSTRACT

The present disclosure relates to methods of identifying patients that may be responsive to mitochondrial inhibitor therapies to target and eradicate cancer stem cells. Also described are diagnostic kits that may be used to identify patients responsive to mitochondrial inhibitor therapies.

CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/508,799, filed May 19, 2017, U.S. Provisional Application No.62/508,788, filed May 19, 2017, U.S. Provisional Application No.62/508,769, filed May 19, 2017, U.S. Provisional Application No.62/508,750, filed May 19, 2017, U.S. Provisional Application No.62/529,871, filed Jul. 7, 2017, U.S. Provisional Application No.62/524,829, filed Jun. 26, 2017, U.S. Provisional Application No.62/576,287, filed October 24, 2017, U.S. Provisional Application No.62/590,432, filed Nov. 24, 2017, and Patent Cooperation TreatyApplication No. PCT/US2018/022403, filed Mar. 14, 2018, the contents ofwhich are incorporated by reference in their entireties. U.S.Provisional Application No. 62/471,688, filed Mar. 15, 2017, is alsoincorporated by reference in its entirety.

FIELD

The present disclosure relates to diagnostic kits and methods foridentifying patients that may be responsive to mitochondrial inhibitortherapies to target and eradicate cancer stem cells.

BACKGROUND

Researchers have struggled to develop new anti-cancer treatments.Conventional cancer therapies (e.g. irradiation, alkylating agents suchas cyclophosphamide, and anti-metabolites such as 5-Fluorouracil) haveattempted to selectively detect and eradicate fast-growing cancer cellsby interfering with cellular mechanisms involved in cell growth and DNAreplication. Other cancer therapies have used immunotherapies thatselectively bind mutant tumor antigens on fast-growing cancer cells(e.g., monoclonal antibodies). Unfortunately, tumors often recurfollowing these therapies at the same or different site(s), indicatingthat not all cancer cells have been eradicated. Relapse may be due toinsufficient chemotherapeutic dosage and/or emergence of cancer clonesresistant to therapy. Hence, novel cancer treatment strategies areneeded.

Advances in mutational analysis have allowed in-depth study of thegenetic mutations that occur during cancer development. Despite havingknowledge of the genomic landscape, modern oncology has had difficultywith identifying primary driver mutations across cancer subtypes. Theharsh reality appears to be that each patient's tumor is unique, and asingle tumor may contain multiple divergent clone cells. What is needed,then, is a new approach that emphasizes commonalities between differentcancer types. Targeting the metabolic differences between tumor andnormal cells holds promise as a novel cancer treatment strategy. Ananalysis of transcriptional profiling data from human breast cancersamples revealed more than 95 elevated mRNA transcripts associated withmitochondrial biogenesis and/or mitochondrial translation. Sotgia etal., Cell Cycle, 11(23):4390-4401 (2012). Additionally, more than 35 ofthe 95 upregulated mRNAs encode mitochondrial ribosomal proteins (MRPs).Proteomic analysis of human breast cancer stem cells likewise revealedthe significant overexpression of several mitoribosomal proteins as wellas other proteins associated with mitochondrial biogenesis. Lamb et al.,Oncotarget, 5(22):11029-11037 (2014).

Functional inhibition of mitochondrial biogenesis using the off-targeteffects of certain bacteriostatic antibiotics or OXPHOS inhibitorsprovides additional evidence that functional mitochondria are requiredfor the propagation of cancer stem cells. The inventors recently showedthat a mitochondrial fluorescent dye (MitoTracker) could be effectivelyused to enrich and purify cancer stem-like cells (CSCs) from aheterogeneous population of living cells. Farnie et al., Oncotarget,6:30272-30486 (2015). Cancer cells with the highest mitochondrial masshad the strongest functional ability to undergo anchorage-independentgrowth, a characteristic normally associated with metastatic potential.The ‘Mito-high’ cell sub-population also had the highesttumor-initiating activity in vivo, as shown using pre-clinical models.The inventors also demonstrated that several classes of non-toxicantibiotics could be used to halt CSC propagation. Lamb et al.,Oncotarget, 6:4569-4584 (2015). Because of the conserved evolutionarysimilarities between aerobic bacteria and mitochondria, certain classesof antibiotics or compounds having antibiotic activity can inhibitmitochondrial protein translation as an off-target side-effect.

SUMMARY

In view of the foregoing background, it is an object of this disclosureto demonstrate methods for identifying a patient for anti-mitochondrialtherapy. Methods may include obtaining a sample from the patient;determining the level of at least one mitochondrial marker in thesample; classifying the patient as a candidate for therapy with ananti-mitochondrial therapy if the sample is determined to have anincreased level of the at least one mitochondrial marker relative to athreshold level. Methods include collecting samples from lung, breast,ovarian, gastric, skin, kidney, pancreas, rectum, colon, prostate,bladder, epithelial, and non-epithelial tissue sample. In someembodiments, the sample is a body fluid such as blood, serum, plasma,saliva, sputum, milk, tears, urine, ascites, cyst fluid, pleural fluid,and cerebral spinal fluid. In some embodiments, the sample includescirculating tumor cells isolated from at least one of serum, plasma, andblood.

The present disclosure includes using mitochondrial protein, RNA, and/orDNA as a mitochondrial marker. The mitochondrial marker may relate to orregulate beta-oxidation and/or ketone metabolism. Such markers includeHSD17B10, BDH1, ACAT1, ACADVL, ACACA, ACLY, HADHB, SUCLG2, ACAD9, HADHA,ECHS1, and ACADSB.

In some embodiments, the mitochondrial marker relates to or regulates atleast one of mitochondrial biogenesis, electron transport, metabolism,ATP synthesis, ADP/ATP exchange/transport, CoQ synthesis, ROSproduction, and suppression of glycolysis, autophagy and/or mitophagy.Such markers include HSPA9, TIMM8A, GFM1, MRPL45, MRPL17, HSPD1(HSP60),TSFM, TUFM, NDUFB10, COX6B1, PMPCA, COX5B, SDHA, UQCRC1, CHCHD2, ATP5B,ATPIF1, ATP5A1, ATP5F1, ATP5H, ATP5O, SLC25A5, COQ9, GPD2, SOGA1, andLRPPRC. In some embodiments, the mitochondrial marker regulates at leastone enzymes ACAT1/2 and/or OXCT1/2.

The present disclosure further relates to methods of administering tothe patient having an increased level of at least one mitochondrialmarker at least mitochondrial inhibitor. The mitochondrial inhibitor maybe a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, atetracycline family member, a erythromycin family member, atovaquone,bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine. Insome embodiments, the tetracycline family member is doxycycline. In someembodiments, the erythromycin family member is azithromycin.

The present disclosure also relates to methods of administering to thepatient an anti-angiogenic agent. Anti-angiogenic agents includeangiostatin, bevacizumab, arresten, canstatin, combretastatin,endostatin, NM-3, thrombospondin, tumstatin, 2-methoxyestradiol,Vitaxin, Getfitinib, ZD6474, erlotinib, CI1033, PKI1666, cetuximab,PTK787, SU6668, SU1 1248, trastuzumab, Marimastat, COL-3, Neovastat,2-ME, SU6668, anti-VEGF antibody, Medi-522 (Vitaxin E), tumstatin,arrestin, recombinant EPO, troponin I, EMD121974, IFN-a celecoxib,PD0332991, tamoxifen, paclitaxel (taxol) and thalidomide. In someembodiments, the anti-angiogenic agent is administered simultaneously orsequentially with a mitochondrial inhibitor.

The present disclosure also relates to diagnostic kits for measuring oneor more mitochondrial markers (companion diagnostics) to identify ahigh-risk cancer patient population that is most likely to benefit fromanti-mitochondrial therapy. In some embodiments, the kit may include acomponent for measuring for measuring levels of mitochondrial markerRNA, DNA, and/or protein relative to a normal control. In someembodiments, the mitochondrial marker is measured by any number of waysknown in the art for measuring RNA, DNA, and or protein, includingquantitative PCR and/or RT-PCR kits, microarrays, Northern blots, andWestern blots. In some embodiments, the kit may include an antibodyspecific to a mitochondrial marker. The antibody may be a monoclonal ora polyclonal antibody. In some embodiments, the kit may include amolecule that binds to at least one of a mitochondrial ribosomal protein(MRP), an OXPHOS complex, and a mitochondrial membraneprotein/chaperone.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-E illustrate the structures of antibiotics that may be usedinhibit the propagation of cancer stem cells (CSCs).

FIGS. 2A-D illustrate the structures of naturally occurring compoundsthat may be used to inhibit the propagation of CSCs.

FIGS. 3A-C illustrate the structures of experimental compounds that maybe used to inhibit the propagation of CSCs.

FIGS. 4A-D illustrate the structure of exemplary mitoriboscins.

FIG. 5 illustrates an exemplary pharmacophore for a mitoketoscin.

FIG. 6A shows a docking image of Compound 2 docking at a succinyl-CoAbinding site of 3-oxoacid CoA-transferase 1 (OXCT1). FIG. 6B shows adocking image of Compound 8 docking at a CoA binding site of humanacetyl-CoA acetyltransferase (ACAT1).

FIG. 7 shows the structures of diphenyleneiodium chloride (DPI) and2-butene-1,4-bis-triphenylphosphonium (TPP).

FIGS. 8A-C show the structures of brutieridin, melitidin, and mDIVI1,respectively.

FIG. 9 provides a summary for personalized cancer diagnosis andtreatment based on mitochondrial-based diagnostics.

FIGS. 10A-B show the probability of recurrence and distant metastasis,respectively, of patients having specific Mito-Signatures.

FIGS. 11A-B show the probability of overall survival in patients havinga specific Mito-Signature and undergoing platin or taxol treatment,respectively.

FIG. 12 shows the basic components of a mitochondrial-based oncologyplatform.

DESCRIPTION

The following description illustrates embodiments of the presentapproach in sufficient detail to enable practice of the presentapproach. Although the present approach is described with reference tothese specific embodiments, it should be appreciated that the presentapproach can be embodied in different forms, and this description shouldnot be construed as limiting any appended claims to the specificembodiments set forth herein. Rather, these embodiments are provided sothat this disclosure will be thorough and complete, and will fullyconvey the scope of the present approach to those skilled in the art.

Tumors and their microenvironment are heterogeneous structures thatbehave like metabolic ecosystems. It is well accepted that more than asingle type of cancer cell exists. For example, within a givenepithelial cancer cell line (such as MCF7 cells), there are “bulk”cancer cells (˜85-95%; the majority of the population), as well asvarious types of progenitor cells (less than 5%), and cancer stem cells(CSCs; less than 1%). CSCs and progenitor cells are thought to be themost dangerous as they behave as tumor-initiating cells (TICs) in vivoand can undergo metastasis. In contrast, “bulk” cancer cells are largelynon-tumorigenic.

Because CSCs are relatively “rare”, little is known about theirmetabolic properties. The inventors previously showed that cells may befunctionally enriched for CSCs by trypsinizing the entire cellpopulation and seeding it as a single-cell suspension ontolow-attachment plates. Under such conditions, the majority (more than90%) of “bulk” cancer cells die via apoptosis, while only the CSCssurvive and propagate, ultimately resulting in the formation of 3Dspheroid structures after about 5 days. Each 3D spheroid is clonallyformed from a single CSC. For breast CSCs, these 3D spheroids are alsoknown as tumor-spheres or mammospheres. The generation of these 3Dspheroids is thought to mimic the process of tumor formation and/ormetastasis, thus providing a model for drug discovery and functionalvalidation.

To understand the metabolic differences between “bulk” cancer cells andCSCs, the inventors previously compared cultured breast cancer cellsgrown either as monolayers or 3D spheroids. These cells were subjectedto profiling via unbiased label-free proteomics analysis. The inventorsfound that over 60 nuclear-encoded mitochondrial proteins werespecifically up-regulated in 3D spheroid structures relative tomonolayer cells processed in parallel. Virtually identical results wereobtained with two distinct ER(+) breast cancer cell lines (MCF7 andT47D; more than 40 overlapping mitochondrial proteins). Informaticsanalysis of the list of up-regulated mitochondrial proteins wasconsistent with an increase in mitochondrial mass, due either to i)increased mitochondrial biogenesis or ii) a shut down in mitophagy, orboth. These results indicate that high mitochondrial mass is acharacteristic feature of the CSC phenotype. These results also suggestthat CSCs are dependent on OXPHOS and/or new mitochondrial biogenesis(protein translation) for survival and propagation. While testing thishypothesis, inventors showed that 3D spheroid formation is effectivelyblocked using specific mitochondrial inhibitors, such as oligomycin,which targets mitochondrial Complex V and shuts off ATP synthesis.However, oligomycin is toxic and cannot be used as an anti-cancertherapeutic. Thus, these results highlight the need for compounds thatcan target mitochondria in CSCs without inducing deleterious sideeffects in normal cells.

To further validate the functional relationship between highmitochondrial mass and “stemness”, inventors employed staining withMitoTracker to metabolically fractionate an MCF7 cell line into“Mito-high” and “Mito-low” cell sub-populations. MitoTracker is anon-toxic fluorescent probe that can be used to directly measuremitochondrial mass in live cells by flow cytometry. As predicted, the“Mito-high” cell population, with increased mitochondrial mass, showedthe greatest capacity for i) 3D spheroid formation and ii) tumorinitiation in a pre-clinical animal model in vivo. Therefore,mitochondrial mass may be a critical determinant of stemness in cancercells. Similarly, elevated telomerase activity (hTERT), a functionalmarker of proliferation and immortality in CSCs, was also specificallyassociated with high mitochondrial mass. The inventors hypothesized thata targeted reduction in mitochondrial mass or OXPHOS may be used toeradicate CSCs.

The inventors have recently focused efforts on the identification andrepurposing of FDA-approved drugs that may be used to inhibit thepropagation of CSCs. These antibiotics include members of thetetracycline family (doxycycline/tigecycline), the erythromycin family(azithromycin), anti-parasitic drugs (pyrvinium pamoate and atovaquone),and antimicrobials targeting drug-resistant mycobacterium (bedaquiline;TB, tuberculosis). FIG. 1 provides exemplary structures of theseantibiotics (FIGS. 1A-E show the structures of doxycycline,azithromycin, pyrvinium (pamoate salt; not shown), atovaquone, andbedaquiline, respectively). Table 1 lists exemplary antibiotics andshows which mitochondrial structure or process is targeted. For example,doxycycline and azithromycin inhibit mitochondrial protein translation,thereby inhibiting mitochondrial biogenesis as an off-target sideeffect. Pyrvinium pamoate and atovaquone inhibit OXPHOS (related tomitochondrial complex II/III) as a side effect. Bedaquiline inhibitsATP-synthase (mitochondrial complex V). Each of these antibiotics hasbeen shown to inhibit anchorage-independent propagation of CSCs bytargeting mitochondrial function.

TABLE 1 Exemplary FDA-approved drugs that may be used to eradicate CSCs.Drug Name Inhibition of FDA-approved Doxycycline Mito Biogenesis YesTigecycline Mito Biogenesis Yes Azithromycin Mito Biogenesis YesPyrvinium pamoate OXPHOS/Complex II Yes Atovaquone OXPHOS/Complex IIIYes Bedaquiline Complex V Yes Palbociclib CDK4/6 Yes

Inventors have also previously identified experimental and naturalcompounds that target CSCs, including glycolysis inhibitors (Vitamin Cand Silibinin), mitochondrial inhibitors (Actinonin; CAPE, from Honeybee propolis), and inhibitors of protein synthesis (puromycin) andNAD(+) recycling (FK-866). As CSCs appear to be highly proliferative,due to their over-expression of telomerase (hTERT), they are sensitiveto Palbociclib, an FDA-approved CDK4/6 inhibitor, with an IC-50 of ˜100nM. Therefore, inhibition of CSC proliferation is an alternative orcould be used in conjunction with other cancer therapies.

Doxycycline shows many other anti-cancer properties that may be furtherexplored. For example, Doxycycline behaves as a radio-sensitizer, makingCSCs approximately 3 to 5 times more sensitive to radiation treatment.In addition, Doxycycline effectively targets hypoxic CSCs and overcomesPaclitaxel-resistance under conditions of hypoxia; this may haveimportant implications for achieving more effective anti-angiogenictherapy. Doxycycline appears to be effective as a mutation-independentapproach for targeting CSCs as it inhibits both activated H-Ras (G12V)and c-Myc oncogenes as well as other environmental oncogenic stimuli(mitochondrial oxidative stress/ROS), via the specific targeting ofmitochondrial biogenesis.

One concern with doxycycline therapy is the potential for thedevelopment of drug-resistance in CSCs. To investigate this issue, theinventors developed and characterized the phenotypic behavior ofDoxy-resistant (DoxyR)-MCF7 cells. The inventors found that DoxyR-CSCsshow a significant shift towards aerobic glycolysis due to a loss ofmitochondrial function, which ultimately results in metabolicinflexibility. (DoxyR)-MCF7 cells showed an up to 35-fold loss ofmitochondrial-DNA encoded proteins (mt-DNA) that are required for OXPHOSactivity, such as MT-ND3, MT-0O2, MT-ATP6 and MT-ATP8. DoxyR-CSCsappeared to be more “quiescent”, with greater than 50% reductions inproliferation and cell migration, as well as a significantly impairedability to form 3D spheroids. The inventors showed that DoxyR-CSCs aresensitive to other metabolic therapies, including inhibitors of i)OXPHOS (Atovaquone, Irinotecan, Sorafenib, Niclosamide), ii) glycolysis(Vitamin C and Stiripentol) and iii) autophagy (Chloroquine). A listingof these drugs and their targets is provided in Table 2. Therefore, theefficacy of doxycycline treatment may be improved by developingcombination therapies with other metabolic inhibitors, based on theconcepts of metabolic inflexibility and synthetic lethality in cancercells.

TABLE 2 Exemplary drugs used in conjugation with doxycycline toeradicate CSCs. Drug Name Target FDA-approved Atovaquone OXPHOS YesIrinotecan OXPHOS Yes Sorafenib OXPHOS Yes Niclosamide OXPHOS YesBerberine OXPHOS Natural supplement 2-deoxy-glucose (2-DG) GlycolysisExperimental Vitamin C Glycolysis Natural supplement StiripentolGlycolysis Clinically-approved (EU/CA/JP) Chloroquine Autophagy Yes

The inventors have also focused efforts on the development oftherapeutics that focus on specific mitochondrial targets. Exemplarytherapeutics are listed in Table 3.

TABLE 3 Exemplary therapeutics that focus on mitochondrial targets.Metabolic Process/ Drug Name Target Mechanism MitoriboscinsMitochondrial Mitochondrial Protein Ribosome Synthesis MitoketoscinsOXCT1/ACAT1 Mitochondrial Ketone Metabolism Mitoflavoscins Mito ComplexVII Flavin-containing proteins (Vit-B2) Tri-phenyl- MitochondriaMitochondrial-targeting- phosphonium (TPP) signal (MTS)

One family of therapeutics, coined “mitoriboscins,” are mito-ribosomeinhibitors that inhibit mitochondrial protein synthesis. FIG. 4A-Dillustrates examples of mitoriboscins. The inventors identified thesecompounds by combining computational chemistry (in silico drug design inwhich the target used was the 3D structure of the large mitochondrialribosome, as determined by cryo-electron microscopy) with phenotypiclibrary screening to detect ATP depletion.

By targeting the mitochondrial enzymes OXCT1 and ACAT1, inventors alsodeveloped mitochondrial inhibitors that interfere with ketone metabolism(these compounds mimic the structure of CoA). These compounds are knownas “mitoketoscins.” FIG. 5 illustrates a pharmacophore for amitoketoscin. FIG. 6A illustrates the docking of Compound 2 (a hit foran OXCT1 screen) at the succinyl-CoA binding site of OXCT1. FIG. 6Billustrates the docking of Compound 8 (a hit for an ACAT1 screen) at theCoA binding site of human ACAT1.

Inventors also identified compounds named “mitoflavoscins,” compoundsthat bind to flavin-containing enzymes and inhibit mitochondrialfunction. Such compounds may be designed to target and deplete FMN, FAD,and/or riboflavin. The inventors identified an approach to acutelyinduce a Vitamin B2 (riboflavin) deficiency that potently inhibits CSCpropagation, with an IC-50 of ˜3 nM. This drug is approximately 30 timesmore potent than Palbociclib for targeting CSCs. FIG. 7 illustrates thestructure of DPI, one embodiment of a mitoflavoscin.

Inventors also identified the use of tri-phenyl-phosphonium (TPP) toeradicate CSCs. TPP behaves as a mitochondrial targeting signal. FIG. 7illustrates the structure of TPP. TPP compounds appear to be able tometabolically distinguish between “normal cell” mitochondria and“malignant” mitochondria of bulk cancer cells and CSCs, as the TPPcompounds are non-toxic in normal human fibroblasts and yet block CSCpropagation.

Inventors also investigated naturally-occurring mitochondrial inhibitorsthat may be used to more effectively target CSCs. A list of exemplarynaturally-occurring mitochondrial inhibitors is provided in Table 4. Theinventors found that brutieridin and melitidin, two compounds found inbergamot, act as statin-like drugs and inhibit mevolonate metabolism aswell as CSC propagation. FIGS. 8A-B illustrate the structures ofbrutieridin and melitidin, respectively. FIG. 8C illustrates thestructure of mDIVI1 for comparison. Interference with the normal processof mitochondrial fission-fusion cycles, such as by targeting the DRP1protein, may represent a viable strategy for eradicating CSCs.

TABLE 4 Naturally-occurring mitochondrial inhibitors that target CSCs.Drug Name Target Metabolic Process Inhibited mDIVI1 DRP1* MitochondrialFission/Fusion Brutieridin HMGR** Mevalonate Metabolism Melitidin HMGR**Mevalonate Metabolism *Dynamin-related protein 1**3-hydroxy-3-methylglutaryl-CoA-reductase.

The identification and design of new mitochondrial inhibitors may haveother medical applications and benefits such as the development of newanti-bacterial and anti-fungal agents and combatingantibiotic-resistance. According to the ndo-symbiotic Theory ofMitochondrial Evolution”, mitochondria first originated historicallyfrom the engulfment of aerobic bacteria, an event that occurred ˜1.45billion years ago. As a result, mitochondria share strong structural andfunctional similarities with bacteria, explaining the off-target effectsof antibiotics, which often show manageable mitochondrial side-effects.Conversely, it would be predicted that mitochondrial inhibitors may alsoshow some moderate anti-bacterial and anti-fungal side effects.

To directly test this hypothesis, the inventors evaluated theanti-bacterial and anti-fungal activity of exemplary mitoriboscins.Several mitoriboscins showed anti-bacterial activity towards bothgram-positive and gram-negative organism(s), pathogenic yeast (Candidaalbicans) and Methicillin-resistant Staphylococcus aureus (MRSA).Therefore, using cancer cells for initial drug screening may also beuseful for developing new antibiotics to combat drug-resistantmicro-organisms.

Over one thousand mitochondrial proteins are encoded by the nucleargenome. The inventors have begun to assess their potential prognosticvalue as biomarkers and companion diagnostics. The inventors hypothesizethat the over-expression of a given mitochondrial protein in cancercells and CSCs may be associated with tumor recurrence and metastasis,due to the emergence of drug resistance, and ultimately resulting intreatment failure. To test this hypothesis, the inventors used an onlinesurvival-analysis tool to perform Kaplan-Meier (K-M) studies on morethan 400 nuclear mitochondrial gene transcripts to interrogate publiclyavailable microarray data from patients with four distinct epithelialcancer types: i) breast, ii) ovarian, iii) lung and iv) gastric. In allfour anatomic cancer types, the inventors observed that theover-expression of mitochondrial gene transcripts is associated withpoor clinical outcome. For example, this approach effectively predictedtamoxifen-resistance in ER(+) breast cancer patients (represented asrecurrence and distant metastasis in FIGS. 10A-B, respectively), as wellas Taxol and Platin resistance in ovarian cancer patients (representedas overall survival in FIGS. 11A-B, respectively). These results arefunctionally supported by further experimental observationsdemonstrating that Tamoxifen-resistant MCF7 cells (TAMR) show asignificant increase in mitochondrial oxygen consumption and ATPproduction.

The present disclosure therefore relates to methods of predicting thesensitivity of neoplastic cell growth to anti-mitochondrial agents. Themethods may include obtaining a sample of a neoplasm from a patient,determining the level of mitochondrial markers in the sample andcomparing the level of mitochondrial markers to a control, andpredicting the sensitivity of the neoplastic cell growth to inhibitionby an anti-mitochondrial agent based on relative marker levels. Highexpression levels of mitochondrial markers correlate with highsensitivity to inhibition by an anti-mitochondrial agent. Mitochondrialmarkers may be obtained from tumor biopsy samples and/or by isolatingcirculating tumor cells from serum, plasma, and/or blood samples.Mitochondrial markers may include mitochondrial RNAs, proteins, and/ormitochondrial DNA. In some embodiments, mitochondrial DNA may beobtained from body fluids (e.g., blood, serum, plasma, saliva, sputum,milk, tears, urine, ascites, cyst fluid, pleural fluid, and/or cerebralspinal fluid). Mitochondrial marker levels may be measured by any numberof ways known in the art, including quantitative PCR and/or RT-PCR,microarrays, Northern blots, Western blots, etc.

In some embodiments, mitochondrial markers may include mitochondrialproteins, RNA, and/or DNA that are associated with or regulatebeta-oxidation and/or ketone metabolism, such as HSD17B10, BDH1, ACAT1,ACADVL, ACACA, ACLY, HADHB, SUCLG2, ACAD9, HADHA, ECHS1, ACADSB. In someembodiments, mitochondrial markers may include mitochondrial proteins,RNA, and/or DNA that are involved in: mitochondrial biogenesis, such asHSPA9, TIMM8A, GFM1, MRPL45, MRPL17, HSPD1(HSP60), TSFM, TUFM; electrontransport, such as NDUFB10, COX6B1, PMPCA, COX5B, SDHA, UQCRC1;metabolism, such as CHCHD2, ATP synthesis, such as ATP5B, ATPIF1,ATP5A1, ATP5F1, ATP5H, ATP5O; ADP/ATP exchange/transport, such asSLC25A5; CoQ synthesis, such as COQ9; ROS production, such as GPD2;and/or suppression of glycolysis, autophagy and mitophagy, such as SOGA1and LRPPRC. In some embodiments, the mitochondrial markers may includemitochondrial proteins, RNA, and/or DNA related to the enzymes ACAT1/2and/or OXCT1/2.

In some embodiments, the mitochondrial markers may include mitochondrialproteins, RNA, and/or DNA that are upregulated or increased in certaincancer types. For example, Table 5, adapted from U.S. ProvisionalApplication No. 62/508,799, the contents of which is incorporated byreference in its entirety, shows exemplary proteins that may be used asmitochondrial biomarkers in gastric cancers. As is shown in Table 5,mitochondrial biomarkers may include mitochondrial proteins, RNA, and/orDNA associated with heat shock proteins and chaperones, membraneproteins, mitochondrial antioxidants, mitochondrial genome maintenance,large and/or small ribosomal subunits, and OXPHOS complexes. In someembodiments, two or more mitochondrial biomarkers may be used to createa “Mito-Signature”, a predictor for clinical outcomes. An exemplaryMito-Signature for gastric cancer is shown in Table 6.

TABLE 5 Prognostic value of mitochondrial markers in gastric cancers.Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Heat Shock Proteins andChaperones (4 probes) 200807_s_at HSPD1 1.83 1.9e−06 200806_s_at HSPD11.56 0.003 200691_s_at HSPA9 1.61 0.0002 205565_s_at FXN 1.38 0.01Membrane Proteins (9 probes) 208844_at VDAC3 2.22 1.4e−09 211662_s_atVDAC2 1.51 0.002 200955_at IMMT 2.20 2.4e−09 218118_s_at TIMM23 1.914.2e−07 218408_at TIMM10 1.88 1.4e−06 218357_s_at TIMM8B 1.49 0.002201821_s_at TIMM17A 1.33 0.025 201870_at TOMM34 1.95 5.1e−07 202264_s_atTOMM40 1.44 0.009 Mitochondrial Anti-Oxidants (2 probes) 215223_s_atSOD2 1.72 2.1e−05 215078_at SOD2 1.70 2.9e−05 Mitochondrial GenomeMaintenance (3 probes) 208694_at PRKDC 2.05 1.2e−07 210543_s_at PRKDC1.78 6.9e−06 215757_at PRKDC 1.47 0.003 Large Ribosomal Subunit (12probes) 204599_s_at MRPL28 2.17 1.2e−08 221997_s_at MRPL52 2.12 3.2e−09222216_s_at MRPL17 1.68 0.0001 220527_at MRPL20 1.67 0.0002 217907_atMRPL18 1.62 0.0004 218887_at MRPL2 1.60 0.0002 203931_s_at MRPL12 1.560.001 208787_at MRPL3 1.53 0.0007 217919_s_at MRPL42 1.52 0.002218049_s_at MRPL13 1.47 0.008 218281_at MRPL48 1.40 0.009 213897_s_atMRPL23 1.29 0.049 Small Ribosomal Subunit (8 probes) 215919_s_at MRPS111.89 5.1e−07 213840_s_at MRPS12 1.84 1.5e−06 210008_s_at MRPS12 1.470.004 204330_s_at MRPS12 1.37 0.015 204331_s_at MRPS12 1.37 0.037203800_s_at MRPS14 1.53 0.002 219220_x_at MRPS22 1.44 0.005 219819_s_atMRPS28 1.42 0.01 218112_at MRPS34 1.36 0.02 Complex I (11 probes)201757_at NDUFS5 2.27   6e−10 215850_s_at NDUFA5 1.93 2.1e−07 208969_atNDUFA9 1.92 1.5e−06 203606_at NDUFS6 1.74 7.9e−05 214241_at NDUFB8 1.675.7e−05 203371_s_at NDUFB3 1.51 0.002 218226_s_at NDUFB4 1.49 0.003202001_s_at NDUFA6 1.37 0.02 218160_at NDUFA8 1.31 0.04 202785_at NDUFA71.31 0.04 218563_at NDUFA3 1.30 0.04 Complex II (1 probe) 214166_at SDHB1.40 0.009 Complex III (2 probes) 207618_s_at BCS1L 1.76 7.1e−06202233_s_at UQCR8 1.51 0.001 Complex IV (10 probes) 213736_at COX5B 2.141.4e−08 218057_x_at COX4NB 1.94 7.7e−07 201754_at COX6C 1.74 7.1e−05201441_at COX6B1 1.67 0.0001 200925_at COX6A1 1.64 8.8e−05 203880_atCOX17 1.60 0.0003 217451_at COX5A 1.49 0.006 202110_at COX7B 1.42 0.01217249_x_at COX7A2 1.33 0.035 216003_at COX10 1.33 0.046 Complex V (13probes) 221677_s_at ATP5O 2.22 2.1e−10 207552_at ATP5G2 1.90 7.5e−06207335_x_at ATP5I 1.84 8.4e−06 217801_at ATP5E 1.64 0.0002 208972_s_atATP5G1 1.51 0.002 210149_s_at ATP5H 1.49 0.003 202961_s_at ATP5J2 1.470.004 210453_x_at ATP5L 1.45 0.006 207573_x_at ATP5L 1.44 0.01208746_x_at ATP5L 1.40 0.009 213366_x_at ATP5C 1.33 0.03 206993_at ATP5S1.29 0.04 213366_x_at ATP5C1 1.33 0.03

TABLE 6 Exemplary compact gastric cancer Mito-Signature for predictingclinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank Test201757_at NDUFS5 2.27  6e−10 208844_at VDAC3 2.22 1.4e−09 221677_s_atATP5O 2.22 2.1e−10 200955_at IMMT 2.20 2.4e−09 204599_s_at MRPL28 2.171.2e−08 213736_at COX5B 2.14 1.4e−08 221997_s_at MRPL52 2.12 3.2e−09208694_at PRKDC 2.05 1.2e−07 Combined 2.77 1.4e−14

In some embodiments, the mitochondrial markers may include mitochondrialproteins, RNA, and/or DNA that are upregulated or increased in ovariancancers. Table 7, adapted from U.S. Provisional Application No.62/508,788, the contents of which is incorporated by reference in itsentirety, shows exemplary proteins that may be used as mitochondrialbiomarkers in ovarian cancers. As is shown in Table 7, mitochondrialbiomarkers may include mitochondrial proteins, RNA, and/or DNAassociated with heat shock proteins and chaperones, membrane proteins,mitochondrial antioxidants, mitochondrial creatine kinases, large and/orsmall ribosomal subunits, and OXPHOS complexes. ExemplaryMito-Signatures for ovarian cancer are shown in Table 8.

TABLE 7 Prognostic value of mitochondrial markers in ovarian cancers.Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Chaperones/HSPs200691_s_at HSPA9 1.77 0.047 Membrane Proteins 200955_at IMMT 2.61 0.002218408_at TIMM10 2.63 0.0008 201821_s_at TIMM17A 2.46 0.003 217981_s_atTIMM10B 1.94 0.05 218118_s_at TIMM23 1.79 0.05 201519_at TOMM70A 2.280.005 211662_s_at VDAC2 2.32 0.01 208845_at VDAC3 2.07 0.01 208846_s_atVDAC3 1.96 0.048 200657_at SLC25A5 2.67 0.0008 221020_s_at SLC25A32 1.980.05 Anti-Oxidant Proteins 201468_s_at NQO1 3.48 0.001 210519_s_at NQO12.37 0.006 215223_s_at SOD2 1.82 0.048 Mitochondrial Creatine Kinase205295_at CKMT2 2.27 0.0035 Large Ribosomal Subunit 201717_at MRPL493.56 4.3e−05 221692_s_at MRPL34 2.99 0.001 218890_x_at MRPL35 2.48 0.002213897_s_at MRPL23 2.48 0.01 217907_at MRPL18 2.36 0.006 218281_atMRPL48 2.29 0.007 222216_s_at MRPL17 2.17 0.007 217980_s_at MRPL16 2.170.008 219162_s_at MRPL11 2.14 0.02 218105_s_at MRPL4 1.90 0.03 SmallRibosomal Subunit 203800_s_at MRPS14 2.97 0.0002 204331_s_at MRPS12 2.90  9e−04 210008_s_at MRPS12 2.46 0.0035 221688_s_at MRPS4 2.88 0.002219819_s_at MRPS28 2.64 0.0008 218001_at MRPS2 2.15 0.01 219220_x_atMRPS22 2.13 0.025 218654_s_at MRPS33 2.05 0.02 217942_at MRPS35 2.050.03 212604_at MRPS31 2.02 0.02 221437_s_at MRPS15 1.88 0.05 Complex I218563_at NDUFA3 3.55 2.3e−05 218320_s_at NDUFB11 3.12   7e−05 201740_atNDUFS3 2.93 0.001 218200_s_at NDUFB2 2.60 0.001 203371_s_at NDUFB3 2.560.0008 203189_s_at NDUFS8 2.43 0.002 218201_at NDUFB2 2.43 0.002203613_s_at NDUFB6 2.43 0.008 202000_at NDUFA6 2.43 0.0015 202785_atNDUFA7 2.30 0.01 220864_s_at NDUFA13 2.25 0.006 209303_at NDUFS4 2.200.009 218160_at NDUFA8 2.16 0.008 203190_at NDUFS8 2.15 0.01 202941_atNDUFV2 2.13 0.02 208714_at NDUFV1 2.07 0.03 209224_s_at NDUFA2 2.030.044 211752_s_at NDUFS7 1.98 0.02 217860_at NDUFA10 1.95 0.037202298_at NDUFA1 1.91 0.03 208969_at NDUFA9 1.89 0.26 201966_at NDUFS21.86 0.035 Complex II 210131_x_at SDHC 2.97 0.0005 202004_x_at SDHC 2.780.0005 202675_at SDHB 1.83 0.04 Complex III 208909_at UQCRFS1 3.689.8e−05 201568_at UQCR7 2.28 0.004 209065_at UQCR6 2.12 0.04 202090_s_atUQCR 1.86 0.04 212600_s_at UQCR2 1.76 0.047 Complex IV 201441_at COX6B2.64 0.0009 203880_at COX17 2.49 0.004 203858_s_at COX10 2.47 0.002211025_x_at COX5B 2.34 0.004 202343_x_at COX5B 2.32 0.004 202110_atCOX7B 2.30 0.02 218057_x_at COX4NB 2.08 0.01 202698_x_at COX4I1 1.890.03 201119_s_at COX8A 1.87 0.04 204570_at COX7A 1.76 0.05 Complex V208870_x_at ATP5C 2.57 0.0008 213366_x_at ATP5C 2.44 0.002 205711_x_atATP5C 2.08 0.01 207507_s_at ATP5G3 2.40 0.002 210453_x_at ATP5L 2.350.003 208746_x_at ATP5L 2.24 0.005 207573_x_at ATP5L 2.20 0.006208972_s_at ATP5G 2.15 0.007 207508_at ATP5G3 2.12 0.01 202961_s_atATP5J2 1.91 0.02 217848_s_at PPA1 1.89 0.03 202325_s_at ATP5J 1.78 0.05

TABLE 8 Exemplary compact ovarian cancer Mito-Signatures for predictingclinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank TestMito-Signature 1 208909_at UQCRFS1 3.68 9.8e−05 201717_at MRPL49 3.564.3e−05 Combination 4.59 3.1e−05 Mito-Signature 2 208909_at UQCRFS1 3.689.8e−05 218563_at NDUFA3 3.55 2.3e−05 Combination 5.03 1.2e−05Mito-Signature 3 208909_at UQCRFS1 3.68 9.8e−05 218563_at NDUFA3 3.552.3e−05 201202_at PCNA 2.85 0.0003 Combination 5.63 7.6e−06

In some embodiments, the mitochondrial markers may include mitochondrialproteins, RNA, and/or DNA that are upregulated or increased in breastcancers. Table 9, adapted from U.S. Provisional Application No.62/508,750, the contents of which is incorporated by reference in itsentirety, shows exemplary proteins that may be used as mitochondrialbiomarkers in breast cancers. As is shown in Table 9, mitochondrialbiomarkers may include mitochondrial proteins, RNA, and/or DNAassociated mitochondrial chaperones, membrane proteins, mitochondrialcarrier families, mitochondrial antioxidants, mitochondrial creatinekinases, large and/or small ribosomal subunits, and OXPHOS complexes.Exemplary Mito-Signatures for breast cancer are shown in Table 10.

TABLE 9 Prognostic value of mitochondrial markers in breast cancers.Gene Probe ID Symbol Hazard-Ratio Log-Rank Test Mito Chaperones200807_s_at HSPD1 3.61 5.9e−06 200806_s_at HSPD1 2.30 0.006 200691_s_atHSPA9 2.04 0.01 205565_s_at FXN 1.83 0.038 221235_s_at TRAP1 1.79 0.047Mito Membrane Proteins 211662_s_at VDAC2 4.17 2.2e−07 210626_at AKAP12.15 0.01 200955_at IMMT 1.81 0.04 201519_at TOMM70A 2.78 0.0003201512_s_at TOMM70A 2.15 0.01 203093_s_at TIMM44 2.23 0.01 218188_s_atTIMM13 2.23 0.02 201822_at TIMM17A 2.01 0.01 215171_s_at TIMM17A 1.850.04 203342_at TIMM17B 1.78 0.04 Mito Carrier Family 217961_at SLC25A382.77 0.0003 210010_s_at SLC25A1 2.38 0.002 200657_at SLC25A5 2.04 0.01221020_s_at SLC25A32 1.98 0.02 Mito Anti-Oxidants 215223_s_at SOD2 2.940.0001 215078_at SOD2 2.81 0.008 Mito Creatine Kinase 205295_at CKMT22.18 0.04 202712_s_at CKMT1A 2.03 0.02 Large Ribosomal Subunit 218027_atMRPL15 3.28 1.6e−05 217907_at MRPL18 2.91 0.0001 219244_s_at MRPL46 2.890.02 218270_at MRPL24 2.38 0.002 218049_s_at MRPL13 2.14 0.01 218281_atMRPL48 2.11 0.01 208787_at MRPL3 2.07 0.03 213897_s_at MRPL23 2.02 0.04218105_s_at MRPL4 1.99 0.02 222216_s_at MRPL17 1.97 0.02 217919_s_atMRPL42 1.88 0.05 218202_x_at MRPL44 1.78 0.04 Small Ribosomal Subunit204330_s_at MRPS12 2.35 0.03 211595_s_at MRPS11 2.26 0.01 219819_s_atMRPS28 1.88 0.03 217919_s_at MRPL42 1.88 0.05 219220_x_at MRPS22 1.850.04 218654_s_at MRPS33 1.84 0.04 Complex I 218160_at NDUFA8 2.45 0.002202000_at NDUFA6 2.41 0.002 202001_s_at NDUFA6 2.23 0.006 203039_s_atNDUFS1 2.40 0.003 201740_at NDUFS3 2.17 0.006 203613_s_at NDUFB6 1.990.02 208714_at NDUFV1 1.96 0.03 203606_at NDUFS6 1.92 0.04 202298_atNDUFA1 1.89 0.03 Complex III 209065_at UQCRB 3.42 1.9e−05 209066_x_atUQCRB 2.12 0.01 205849_s_at UQCR6 2.53 0.002 201066_at UQCR4 1.96 0.02212600_s_at UQCRC2 1.92 0.04 Complex IV 203880_at COX17 2.99 7.6e−05213735_s_at COX5B 2.51 0.001 202343_x_at COX5B 2.10 0.01 211025_x_atCOX5B 2.08 0.01 202698_x_at COX4I1 2.36 0.02 200925_at COX6A1 2.14 0.01218057_x_at COX4NB 1.99 0.04 217249_x_at COX7A2 1.90 0.03 Complex V202325_s_at ATP5J 2.65 0.01 202961_s_at ATP5J2 2.44 0.035 213366_x_atATP5C1 2.19 0.01 208870_x_at ATP5C1 2.08 0.01 205711_x_at ATP5C1 2.000.02 217848_s_at PPA1 2.07 0.01 221677_s_at ATP5O 2.03 0.02 217801_atATP5E 1.99 0.02 207508_at ATP5G3 1.93 0.02

TABLE 10 Exemplary compact breast cancer Mito-Signatures for predictingclinical outcome. Gene Probe ID Symbol Hazard-Ratio Log-Rank TestMito-Signature 1 200807_s_at HSPD1 3.61 5.9e−06 209065_at UQCRB 3.421.9e−05 218027_at MRPL15 3.28 1.6e−05 203880_at COX17 2.99 7.6e−05Combined 5.34   1e−09 Mito-Signature 2 211662_s_at VDAC2 4.17 2.2e−07200807_s_at HSPD1 3.61 5.9e−06 Combined 5.19   6e−09

In some embodiments, the mitochondrial markers may include mitochondrialproteins, RNA, and/or DNA that are upregulated or increased in lungcancers. Table 11, adapted from U.S. Provisional Application No.62/508,769, the contents of which is incorporated by reference in itsentirety, shows exemplary proteins that may be used as mitochondrialbiomarkers in lung cancers. As is shown in Table 11, mitochondrialbiomarkers may include mitochondrial proteins, RNA, and/or DNAassociated with mitochondrial heat shock proteins and membrane proteins,mitochondrial creatine kinases, mitochondrial genome maintenanceproteins, large and/or small ribosomal subunits, and OXPHOS complexes.

TABLE 11 Prognostic value of mitochondrial markers in lung cancers. GeneProbe ID Symbol Hazard-Ratio Log-Rank Test HSPs and Membrane Proteins(28 probes in total) 200806_s_at HSPD1 4.89 <1.0e−16  218119_at TIMM234.68 1.1e−16 218357_s_at TIMM8B 4.26 7.8e−16 203342_at TIMM17B 3.312.5e−11 203093_s_at TIMM44 2.29 1.1e−09 217981_s_at TIMM10B 2.15 1.2e−06218316_at TIMM9 2.06 4.3e−08 201821_s_at TIMM17A 2.04 1.7e−09218188_s_at TIMM13 1.94 8.5e−09 218118_s_at TIMM23 1.83 1.8e−07218408_at TIMM10 1.79   4e−05 202264_s_at TOMM40 4.29 1.1e−14217960_s_at TOMM22 3.19 1.3e−13 201870_at TOMM34 2.83 9.8e−12201812_s_at TOMM7 2.84 5.4e−13 201512_s_at TOMM70A 1.90 3.1e−08212773_s_at TOMM20 1.54 0.0006 217139_at VDAC1 3.74 1.9e−14 217140_s_atVDAC1 2.58 1.1e−16 212038_s_at VDAC1 1.63 7.8e−05 208844_at VDAC3 3.643.9e−14 211662_s_at VDAC2 2.36   6e−14 210625_s_at AKAP1 1.88 1.3e−06200657_at SLC25A5 1.54 0.0001 Mitochondrial Creatine Kinase (2 probes intotal) 202712_s_at CKMT1A 2.88 7.8e−10 205295_at CKMT2 1.51 0.0005Mitochondrial Genome Maintenance (3 probes in total) 210543_s_at PRKDC4.69 1.1e−16 208694_at PRKDC 2.23 4.3e−12 215757_at PRKDC 1.65 4.0e−05Large Ribosomal Subunit (21 probes in total) 218281_at MRPL48 4.361.9e−15 213897_s_at MRPL23 3.55 5.4e−13 219162_s_at MRPL11 3.29 2.5e−13221997_s_at MRPL52 3.20 3.6e−14 221692_s_at MRPL34 3.08 1.6e−11203931_s_at MRPL12 2.82 3.3e−12 218887_at MRPL2 2.81 4.4e−11 217919_s_atMRPL42 2.54 1.6e−13 218270_at MRPL24 2.35 1.8e−09 218105_s_at MRPL4 2.321.6e−09 218202_x_at MRPL44 2.19 2.5e−10 222216_s_at MRPL17 2.02 1.4e−08218890_x_at MRPL35 1.96 5.7e−09 204599_s_at MRPL28 1.91 1.4e−07220527_at MRPL20 1.84 9.1e−05 201717_at MRPL49 1.68 8.7e−06 218049_s_atMRPL13 1.68 8.1e−06 217980_s_at MRPL16 1.66 1.5e−05 203152_at MRPL401.62 0.0001 218027_at MRPL15 1.59 0.0001 203781_at MRPL33 1.47 0.001 Small Ribosomal Subunit (19 probes in total) 204331_s_at MRPS12 4.101.1e−16 210008_s_at MRPS12 3.93 4.9e−14 204330_s_at MRPS12 3.27   1e−13213840_s_at MRPS12 2.99 2.3e−12 217932_at MRPS7 3.55 2.3e−12 218001_atMRPS2 3.28   1e−11 221688_s_at MRPS4 3.09 7.7e−11 211595_s_at MRPS112.96 9.1e−12 215919_s_at MRPS11 1.55 0.0002 218112_at MRPS34 2.437.6e−08 212604_at MRPS31 2.29 2.7e−07 219819_s_at MRPS28 1.74 2.7e−06217942_at MRPS35 1.70 8.4e−06 221437_s_at MRPS15 1.59 0.0001 12145_atMRPS27 1.61 7.4e−05 218398_at MRPS30 1.47 0.003  218654_s_at MRPS33 1.350.01  203800_s_at MRPS14 1.27 0.05  Complex I (27 probes in total)203371_s_at NDUFB3 4.30 3.6e−15 203189_s_at NDUFS8 4.15 4.4e−16203190_at NDUFS8 2.94 2.1e−11 209303_at NDUFS4 3.83 1.1e−15 218484_atNDUFA4L2 3.33 2.1e−13 218226_s_at NDUFB4 3.21 1.8e−14 220864_s_atNDUFA13 3.00 9.5e−11 202941_at NDUFV2 3.00 1.3e−13 201740_at NDUFS3 2.921.2e−11 217860_at NDUFA10 2.77   3e−14 218563_at NDUFA3 2.23 1.9e−10214241_at NDUFB8 2.23 1.5e−09 218201_at NDUFB2 2.21 1.2e−08 215850_s_atNDUFA5 1.83 3.6e−07 202785_at NDUFA7 1.81   3e−07 202298_at NDUFA1 1.72  3e−06 201966_at NDUFS2 1.70 6.6e−06 202839_s_at NDUFB7 1.64 0.0009201757_at NDUFS5 1.64 4.3e−05 209224_s_at NDUFA2 1.59 6.6e−05 208969_atNDUFA9 1.56 0.0002 211752_s_at NDUFS7 1.50 0.0007 203613_s_at NDUFB61.49 0.0009 209223_at NDUFA2 1.49 0.0009 218320_s_at NDUFB11 1.48 0.001 218200_s_at NDUFB2 1.48 0.001  208714_at NDUFV1 1.44 0.002  Complex II(5 probes in total) 216591_s_at SDHC 4.27 7.8e−16 202004_x_at SDHC 3.64  4e−14 210131_x_at SDHC 3.45 4.2e−14 202675_at SDHB 2.06 7.4e−07214166_at SDHB 1.94 2.5e−08 Complex III (8 probes in total) 201568_atUQCR7 3.34 3.7e−13 209066_x_at UQCR6 2.96 2.5e−10 202233_s_at UQCR8 2.095.9e−07 208909_at UQCRFS1 1.69 2.6e−05 201066_at UQCR4/CYC1 1.54 0.0006207618_s_at BCS1L 1.54 0.0003 205849_s_at UQCR6 1.48 0.0008 202090_s_atUQCR 1.45 0.004  Complex IV (19 probes in total) 211025_x_at COX5B 4.465.3e−15 202343_x_at COX5B 3.97 1.1e−16 213735_s_at COX5B 2.15 9.6e−10213736_at COX5B 1.51 0.0015 200925_at COX6A 3.94 1.1e−16 201119_s_atCOX8A 3.78 2.4e−15 203880_at COX17 3.55 3.9e−15 201754_at COX6C 3.241.8e−14 217249_x_at COX7A2 3.05 3.3e−13 201441_at COX6B 2.93 3.8e−12206353_at COX6A2 2.77 1.8e−11 203858_s_at COX10 2.44 1.3e−09 202110_atCOX7B 2.29 2.5e−12 216003_at COX10 2.18 1.8e−07 221550_at COX15 2.091.5e−10 217451_at COX5A 2.01   9e−06 218057_x_at COX4NB 1.54 0.0008204570_at COX7A 1.51 0.0015 202698_x_at COX4I1 1.39 0.01  Complex V (23probes in total) 202961_s_at ATP5J2 4.38 1.3e−14 207507_s_at ATP5G3 4.14 <1e−17 207508_at ATP5G3 2.34 1.6e−13 210149_s_at ATP5H 3.70 3.7e−15209492_x_at ATP5I 3.33 7.7e−13 207335_x_at ATP5I 2.14   2e−08203926_x_at ATP5D 3.02 2.7e−11 213041_s_at ATP5D 2.41 3.1e−10208764_s_at ATP5G2 2.75 2.9e−10 207552_at ATP5G2 2.55 4.3e−09 217368_atATP5G2 1.85 4.9e−07 217801_at ATP5E 2.62   2e−09 210453_x_at ATP5L 2.561.8e−11 207573_x_at ATP5L 2.25 1.9e−10 208746_x_at ATP5L 2.10 7.4e−10201322_at ATP5B 1.88 1.5e−07 206992_s_at ATP5S 1.88 2.9e−07 206993_atATP5S 1.85 2.1e−07 208972_s_at ATP5G 1.87 5.4e−08 221677_s_at ATP5O 1.716.8e−06 208870_x_at ATP5C 1.54 0.0008 205711_x_at ATP5C 1.42 0.004 213366_x_at ATP5C 1.40 0.007 

The present disclosure also relates to methods of treating a neoplasticdisease in a patient. Such treatment may occur following thedetermination of increased expression levels of one or moremitochondrial markers. Methods may include obtaining a sample of aneoplasm from a neoplastic disease patient, determining the expressionlevel of one or more mitochondrial markers in the CSCs (e.g.,Mito-signature) of the neoplasm sample relative to a control sample,and, if the higher expression levels of one or more mitochondrialmarkers is detected, administering to the patient a therapeuticallyeffective amount of an anti-mitochondrial agent. The anti-mitochondrialagent may include one or more mitoriboscins, mitoketoscins, and/orantimitoscins. The anti-mitochondrial agent may include compounds thatinhibit mitochondrial function as an off-target effect, such asmetformin, tetracycline family members (such as doxycycline),erythromycin family members (such as azithromycin), atovaquone,bedaquiline. In some embodiments, the anti-mitochondrial agent comprisesa lactate transporter inhibitor or a glycolysis inhibitor. In someembodiments, the glycolysis inhibitor comprises an agent which inhibitstriose-phosphate isomerase, fructose 1,6 bisphosphate aldolase,glycero-3-phosphate dehydrogenase, phosphoglycerate kinase,phosphoglycerate mutase, enolase, pyruvate kinase, and/or lactatedehydrogenase.

In some embodiments, the neoplastic disease is a breast neoplasm subtypesuch as ER(+), PR(+), HER2(+), triple-negative (ER(−)/PR(−)/HER2(−)),ER(−), PR(−), any neoplasm and nodal stages, and any neoplasm grades.The neoplasm may include Luminal A, Luminal B, and Basal breast cancers.In some embodiments, wherein the neoplasm is a pre-malignant lesion suchas a ductal carcinoma in situ (DCIS) of the breast or myelodysplasticsyndrome of the bone marrow. In some embodiments, the neoplasm may befrom a tissue including breast, skin, kidney, lung, pancreas, gastric,rectum and colon, prostate, ovarian, and bladder, and may includeepithelial cells, non-epithelial cells, lymphomas, sarcomas, andmelanomas.

In some embodiments, a patient may be treated with an anti-mitochondrialagent concurrently with an anti-angiogenic agent and/or ananti-neoplastic agent. For example, patients may be treated with ananti-mitochondrial agent in addition to treatment with a conventionalcancer therapy, as is outline in FIG. 9. In some embodiments, one ormore anti-neoplastic agents and/ or anti-angiogenic agents may beadministered simultaneously to or sequentially with theanti-mitochondrial agent. Anti-angiogenic agents may include one or moreof angiostatin, bevacizumab, arresten, canstatin, combretastatin,endostatin, NM-3, thrombospondin, tumstatin, 2-methoxyestradiol,Vitaxin, Getfitinib, ZD6474, erlotinib, CI1033, PKI1666, cetuximab,PTK787, SU6668, SU1 1248, trastuzumab, Marimastat, COL-3, Neovastat,2-ME, SU6668, anti-VEGF antibody, Medi-522 (Vitaxin E), tumstatin,arrestin, recombinant EPO, troponin I, EMD121974, IFN-α celecoxib,PD0332991, tamoxifen, paclitaxel (taxol) and thalidomide.Anti-neoplastic agents may include natural products such as vitamin C,caffeic acid phenyl ester (CAPE), and/or berberine. The anti-neoplasticagent may include one or more of 17-AAG, Apatinib, Ascomycin, Axitinib,Bexarotene, Bortezomib, Bosutinib, Bryostatin 1, Bryostatin 2,Canertinib, Carboplatin, Cediranib, Cisplatin, Cyclopamine, Dasatinib,17-DMAG, Docetaxel, Doramapimod, Dovitinib, Erlotinib, Everolimus,Gefitinib, Geldanamycin, Gemcitabine, Imatinib, Imiquimod, Ingenol3-Angelate, Ingenol 3-Angelate 20-Acetate, Irinotecan, Lapatinib,Lestaurtinib, Nedaplatin, Masitinib, Mubritinib, Nilotinib, NVP-BEZ235,OSU-03012, Oxaliplatin, Paclitaxel, Palbociclib (and other CDK4/6inhibitors), Pazopanib, Picoplatin, Pimecrolimus, PKC412, Rapamycin,Satraplatin, Sorafenib, Sunitinib, Tandutinib, Tivozanib, Thalidomide,Temsirolimus, Tozasertib, Vandetanib, Vargatef, Vatalanib, Zotarolimus,ZSTK474, Bevacizumab (Avasti), Cetuximab, Herceptin, Rituximab,Tamoxifen, Trastuzumab, Apatinib, Axitinib, Bisindolylmaleimide I,Bisindolylmaleimide I, Bosutinib, Canertinib, Cediranib, Chelerythrine,CP690550, Dasatinib, Dovitinib, Erlotinib, Fasudil, Gefitinib,Genistein, Go 6976, H-89, HA-1077, Imatinib, K252a, K252c, Lapatinib,Di-p- Toluenesulfonate, Lestaurtinib, LY 294002, Masitinib, Mubritinib,Nilotinib, OSU-03012, Pazopanib, PD 98059, PKC412, Roscovitine, SB202190, SB 203580, Sorafenib, SP600125, Staurosporine, Sunitinib,Tandutinib, Tivozanib, Tozasertib, Tyrphostin AG 490, Tyrphostin AG1478, U0126, Vandetanib, Vargatef, Vatalanib, Wortmannin, ZSTK474,Cyclopamine, Carboplatin, Cisplatin, Eptaplatin, Nedaplatin,Oxaliplatin, Picoplatin, Satraplatin, Bortezomib (Velcade), Metformin,Halofuginone. Metformin, N-acetyl-cysteine (NAC), RTA 402 (Bardoxolonemethyl), Auranofin, BMS-345541, IMD-0354, PS-1145, TPCA-I,Wedelolactone, Echinomycin, 2-deoxy-D-glucose (2-DG), 2-bromo-D-glucose,2-fluoro-D-glucose, and 2-iodo- D-glucose, dichloro-acetate (DCA),3-chloro-pyruvate, 3-Bromo-pyruvate (3-BrPA), 3-Bromo- 2-oxopropionate,Oxamate, LY 294002, NVP-BEZ235, Rapamycin, Wortmannin, Quercetin,Resveratrol, N-acetyl-cysteine (NAC), N-acetyl-cysteine amide (NACA),Ascomycin, CP690550, Cyclosporin A, Everolimus, Fingolimod, FK-506,Mycophenolic Acid, Pimecrolimus, Rapamycin, Temsirolimus, Zotarolimus,Roscovitine, PD 0332991 (CDK4/6 inhibitor), Chloroquine, BSI-201 ,Olaparib, DR 2313, and NU 1025.

The present disclosure relates to diagnostic kits that may be used toassay a cancer sample for sensitivity to mitochondrial inhibitortherapy. In some embodiments, this kit or platform, known asMITO-ONC-RX, includes both therapeutic and diagnostic modalities (FIG.12). In some embodiments, the present disclosure includes a kit formeasuring one or more mitochondrial markers (companion diagnostics) toidentify a high-risk cancer patient population that is most likely tobenefit from anti-mitochondrial therapy. In some embodiments, the kitmay include a component for measuring for measuring levels ofmitochondrial marker RNA, DNA, and/or protein relative to a normalcontrol. In some embodiments, the mitochondrial marker is measured byany number of ways known in the art for measuring RNA, DNA, and orprotein, including quantitative PCR and/or RT-PCR kits, microarrays,Northern blots, and Western blots. In some embodiments, the kit mayinclude an antibody specific to a mitochondrial marker. The antibody maybe a monoclonal or a polyclonal antibody. In some embodiments, the kitmay include a molecule that binds to at least one of a mitochondrialribosomal protein (MRP), an OXPHOS complex, and a mitochondrial membraneprotein/chaperone.

The terminology used in the description of the invention herein is forthe purpose of describing particular embodiments only and is notintended to be limiting of the invention. As used in the description ofthe invention and the appended claims, the singular forms “a,” “an” and“the” are intended to include the plural forms as well, unless thecontext clearly indicates otherwise. The invention includes numerousalternatives, modifications, and equivalents as will become apparentfrom consideration of the following detailed description.

It will be understood that although the terms “first,” “second,”“third,” “a),” “b),” and “c),” etc. may be used herein to describevarious elements of the invention should not be limited by these terms.These terms are only used to distinguish one element of the inventionfrom another. Thus, a first element discussed below could be termed anelement aspect, and similarly, a third without departing from theteachings of the present invention. Thus, the terms “first,” “second,”“third,” “a),” “b),” and “c),” etc. are not intended to necessarilyconvey a sequence or other hierarchy to the associated elements but areused for identification purposes only. The sequence of operations (orsteps) is not limited to the order presented in the claims.

Unless otherwise defined, all terms (including technical and scientificterms) used herein have the same meaning as commonly understood by oneof ordinary skill in the art to which this invention belongs. It will befurther understood that terms, such as those defined in commonly useddictionaries, should be interpreted as having a meaning that isconsistent with their meaning in the context of the present applicationand relevant art and should not be interpreted in an idealized or overlyformal sense unless expressly so defined herein. The terminology used inthe description of the invention herein is for the purpose of describingparticular embodiments only and is not intended to be limiting of theinvention. All publications, patent applications, patents and otherreferences mentioned herein are incorporated by reference in theirentirety. In case of a conflict in terminology, the presentspecification is controlling.

Also, as used herein, “and/or” refers to and encompasses any and allpossible combinations of one or more of the associated listed items, aswell as the lack of combinations when interpreted in the alternative(“or”).

Unless the context indicates otherwise, it is specifically intended thatthe various features of the invention described herein can be used inany combination. Moreover, the present invention also contemplates thatin some embodiments of the invention, any feature or combination offeatures set forth herein can be excluded or omitted. To illustrate, ifthe specification states that a complex comprises components A, B and C,it is specifically intended that any of A, B or C, or a combinationthereof, can be omitted and disclaimed.

As used herein, the transitional phrase “consisting essentially of” (andgrammatical variants) is to be interpreted as encompassing the recitedmaterials or steps “and those that do not materially affect the basicand novel characteristic(s)” of the claimed invention. Thus, the term“consisting essentially of” as used herein should not be interpreted asequivalent to “comprising.”

The term “about,” as used herein when referring to a measurable value,such as, for example, an amount or concentration and the like, is meantto encompass variations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% ofthe specified amount. A range provided herein for a measurable value mayinclude any other range and/or individual value therein.

Having thus described certain embodiments of the present invention, itis to be understood that the invention defined by the appended claims isnot to be limited by particular details set forth in the abovedescription as many apparent variations thereof are possible withoutdeparting from the spirit or scope thereof as hereinafter claimed.

What is claimed is:
 1. A method for identifying a breast cancer patientfor anti-mitochondrial therapy, the method comprising: obtaining abreast tumor sample obtained from the patient; determining a level of atleast one mitochondrial marker having prognostic value for breast cancermetastasis and recurrence selected from: at least one prognosticmitochondrial chaperone protein or mRNA selected from HSPD1, HSPA9, FXN,and TRAP1; at least one prognostic mitochondrial membrane protein ormRNA selected from VDAC2, AKAP1, IMMT, TOMM70A, TIMM44, TIMM13, TIMM17A,TIMM17A, TIMM17B; at least one prognostic mitochondrial carrier familyprotein or mRNA selected from SLC25A38, SLC25A1, SLC25A5, SLC25A32; theprognostic mitochondrial antioxidant protein or mRNA SOD2; at least oneprognostic mitochondrial creatine kinase selected from CKMT2 and CKMT1A;at least one prognostic large mitochondrial ribosomal subunit protein ormRNA selected from MRPL15, MRPL18, MRPL46, MRPL24, MRPL13, MRPL48,MRPL3, MRPL23, MRPL4, MRPL17, MRPL42, and MRPL44; at least oneprognostic small mitochondrial ribosomal subunit protein or mRNAselected from MRPS12, MRPS11, MRPS28, MRPL42, MRPS22, and MRPS33; atleast one prognostic OXPHOS complex I subunit protein or mRNA selectedfrom NDUFA8, NDUFA6, NDUFS1, NDUFS3, NDUFB6, NDUFV1, NDUFS6, and NDUFA1;at least one prognostic OXPHOS complex III subunit protein or mRNAselected from UQCRB, UQCR6, UQCR4, and UQCRC2; at least one prognosticOXPHOS complex IV subunit protein or mRNA selected from COX17, COX5B,COX4I1, COX6A1, COX4NB, and COX7A2; and at least one OXPHOS complex Vsubunit selected from ATP5J, ATP5J2, ATP5C1, ATP5C1, ATP5C1, PPA1,ATP50, ATP5E, and ATP5G3; classifying the patient as a candidate fortherapy with an anti-mitochondrial therapy, wherein a patient isclassified as a candidate for therapy with an anti-mitochondrial therapyif the sample is determined to have an increased level of the at leastone mitochondrial marker relative to a threshold level; and if thepatient is classified as a candidate for anti-mitochondrial therapy,administering at least one mitochondrial inhibitor.
 2. The method ofclaim 1, wherein the mitochondrial inhibitor inhibits the propagation ofbreast cancer stem cells.
 3. The method of claim 2, wherein the breastcancer stem cells comprise drug-resistant stem cells, and furthercomprising administering at least one of an OXPHOS inhibitor, aglycolysis inhibitor, and an autophagy inhibitor.
 4. The method of claim1, wherein the at least one mitochondrial inhibitor comprises at leastone mitochondrial biogenesis inhibitor and at least one of an OXPHOSinhibitor, a glycolysis inhibitor, and an autophagy inhibitor.
 5. Themethod of claim 1, wherein the mitochondrial inhibitor is at least oneof a mitoriboscin, a mitoketoscin, a antimitoscin, metformin, atetracycline family member, a erythromycin family member, atovaquone,bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine.
 6. Themethod of claim 1, wherein the at least one mitochondrial marker havingprognostic value for breast cancer metastasis and recurrence comprisesat least one of HSPD1, UQCRB, MRPL15, and COX17.
 7. The method of claim1, wherein the at least one mitochondrial marker having prognostic valuefor breast cancer metastasis and recurrence comprises at least twoprognostic markers selected from HSPD1, UQCRB, MRPL15, and COX17.
 8. Themethod of claim 1, wherein the at least one mitochondrial marker havingprognostic value for breast cancer metastasis and recurrence comprisesthe combination of HSPD1, UQCRB, MRPL15, and COX17.
 9. The method ofclaim 1, wherein the at least one mitochondrial marker having prognosticvalue for breast cancer metastasis and recurrence comprises thecombination of VDAC2 and HSPD1.
 10. The method of claim 1, furthercomprising determining a level of at least two mitochondrial markerhaving prognostic value for breast cancer metastasis and recurrence. 11.The method of claim 1, further comprising determining a level of atleast three mitochondrial markers having prognostic value for breastcancer metastasis and recurrence.
 12. A method for identifying a lungcancer patient for anti-mitochondrial therapy, the method comprising:obtaining a lung tumor sample obtained from the patient; determining alevel of at least one mitochondrial marker having prognostic value forlung cancer metastasis and recurrence selected from: at least oneprognostic mitochondrial heat shock protein or mRNA or mitochondrialmembrane protein or mRNA selected from HSPD1, TIMM23, TIMM8B, TIMM17B,TIMM44, TIMM10B, TIMM9, TIMM17A, TIMM13, TJMM23, TIMM10, TOMM40, TOMM22,TOMM34, TOMM7, TOMM70A, TOMM20, VDAC1, VDAC3, VDAC2, AKAP1, and SLC25A5;at least one prognostic mitochondrial creatine kinase selected fromCKMT1A and CKMT2; at least one prognostic mitochondrial genomemaintenance protein or mRNA selected from PRKDC, PRKDC, and PRKDC; atleast one prognostic large mitochondrial ribosomal subunit protein ormRNA selected from MRPL48, MRPL23, MRPL11, MRPL52, MRPL34, MRPL12,MRPL2, MRPL42, MRPL24, MRPL4, MRPL44, MRPL17, MRPL35, MRPL28, MRPL20,MRPL49, MRPL13, MRPL16, MRPL40, MRPL15, and MRPL33; at least oneprognostic small mitochondrial ribosomal subunit protein or mRNAselected from MRPS12, MRPS12, MRPS12, MRPS12, MRPS7, MRPS2, MRPS4,MRPS11, MRPS34, MRPS31, MRPS28, MRPS35, MRPS15, MRPS27, MRPS30, MRPS33,and MRPS14; at least one prognostic OXPHOS complex I subunit protein ormRNA selected from NDUFB3, NDUFS8, NDUFS8, NDUFS4, NDUFA4L2, NDUFB4,NDUFA13, NDUFV2, NDUFS3, NDUFA10, NDUFA3, NDUFB8, NDUFB2, NDUFA5,NDUFA7, NDUFA1, NDUFS2, NDUFB7, NDUFS5, NDUFA2, NDUFA9, NDUFS7, NDUFB6,NDUFA2, NDUFB11, NDUFB2, and NDUFV1; at least one prognostic OXPHOScomplex II subunit protein or mRNA selected from SDHC and SDHB; at leastone prognostic OXPHOS complex III subunit protein or mRNA selected fromUQCR7, UQCR6, UQCR8, UQCRFS1, UQCR4/CYCI, BCS1L, and UQCR; at least oneprognostic OXPHOS complex IV subunit protein or mRNA selected fromCOX5B, COX6A, COX8A, COX17, COX6C, COX7A2, COX6B, COX6A2, COX10, COX7B,COX10, COX15, COX5A, COX4NB, COX7A, and COX4I1; at least one prognosticOXPHOS complex V subunit protein or mRNA selected from ATP5J2, ATP5G3,ATP5H, ATP5I, ATP5D, ATP5G2, ATP5E, ATPSL, ATP5B, ATP5S, ATP5G, ATP5O,and ATP5C; classifying the patient as a candidate for therapy with ananti-mitochondrial therapy, wherein a patient is classified as acandidate for therapy with an anti-mitochondrial therapy if the sampleis determined to have an increased level of the at least onemitochondrial marker relative to a threshold level; and if the patientis classified as a candidate for anti-mitochondrial therapy,administering at least one mitochondrial inhibitor.
 13. The method ofclaim 12, wherein the mitochondrial inhibitor inhibits the propagationof lung cancer stem cells.
 14. The method of claim 13, wherein the lungcancer stem cells comprise drug-resistant stem cells, and furthercomprising administering at least one of an OXPHOS inhibitor, aglycolysis inhibitor, and an autophagy inhibitor.
 15. The method ofclaim 12, wherein the at least one mitochondrial inhibitor comprises atleast one mitochondrial biogenesis inhibitor and at least one of anOXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.16. The method of claim 12, wherein the mitochondrial inhibitor is atleast one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin,a tetracycline family member, a erythromycin family member, atovaquone,bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine. 17.The method of claim 12, further comprising determining a level of atleast two mitochondrial marker having prognostic value for lung cancermetastasis and recurrence.
 18. The method of claim 12, furthercomprising determining a level of at least three mitochondrial markershaving prognostic value for lung cancer metastasis and recurrence.
 19. Amethod for identifying a gastric cancer patient for anti-mitochondrialtherapy, the method comprising: obtaining a gastric tumor sampleobtained from the patient; determining a level of at least onemitochondrial marker having prognostic value for gastric cancermetastasis and recurrence selected from: at least one prognostic heatshock protein or mRNA or mitochondrial chaperone protein or mRNAselected from HSPD1, HSPA9, and FXN; at least one prognosticmitochondrial membrane protein or mRNA selected from VDAC3, VDAC2, IMMT,TIMM23, TIMM10, TTMM8B, TIMM17A, TOMM34, and TOMM40; a prognosticmitochondrial antioxidant protein or mRNA comprising SOD2; a prognosticmitochondrial genome maintenance protein or mRNA comprising PRKDC; atleast one prognostic large mitochondrial ribosomal subunit protein ormRNA selected from MRPL28, MRPL52, MRPL17, MRPL20, MRPL18, MRPL2,MRPL12, MRPL3, MRPL42, MRPL13, MRPL48, and MRPL23; at least oneprognostic small mitochondrial ribosomal subunit protein or mRNAselected from MRPS11, MRPS12, MRPS14, MRPS22, MRPS28, and MRPS34; atleast one prognostic OXPHOS complex I subunit protein or mRNA selectedfrom NDUFS5, NDUFA5, NDUFA9, NDUFS6, NDUFB8, NDUFB3, NDUFB4, NDUFA6,NDUFA8, NDUFA7, and NDUFA3; a prognostic OXPHOS complex II subunitprotein or mRNA comprising SDHB; at least one prognostic OXPHOS complexIII subunit protein or mRNA selected from BCS1L and UQCR8; at least oneprognostic OXPHOS complex IV subunit protein or mRNA selected fromCOX5B, COX4NB, COX6C, COX6B1, COX6A1, COX17, COX5A, COX7B, COX7A2, andCOX10; at least one prognostic OXPHOS complex V subunit protein or mRNAselected from ATP5O, ATP5G2, ATP5I, ATP5E, ATP5G1, ATP5H, ATP5J2, ATP5L,ATP5C, ATP5S, and ATP5C1; classifying the patient as a candidate fortherapy with an anti-mitochondrial therapy, wherein a patient isclassified as a candidate for therapy with an anti-mitochondrial therapyif the sample is determined to have an increased level of the at leastone mitochondrial marker relative to a threshold level; and if thepatient is classified as a candidate for anti-mitochondrial therapy,administering at least one mitochondrial inhibitor.
 20. The method ofclaim 19, wherein the mitochondrial inhibitor inhibits the propagationof gastric cancer stem cells.
 21. The method of claim 20, wherein thegastric cancer stem cells comprise drug-resistant stem cells, andfurther comprising administering at least one of an OXPHOS inhibitor, aglycolysis inhibitor, and an autophagy inhibitor.
 22. The method ofclaim 19, wherein the at least one mitochondrial inhibitor comprises atleast one mitochondrial biogenesis inhibitor and at least one of anOXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.23. The method of claim 19, wherein the mitochondrial inhibitor is atleast one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin,a tetracycline family member, a erythromycin family member, atovaquone,bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine. 24.The method of claim 19, further comprising determining a level of atleast two mitochondrial marker having prognostic value for gastriccancer metastasis and recurrence.
 25. The method of claim 19, furthercomprising determining a level of at least three mitochondrial markershaving prognostic value for gastric cancer metastasis and recurrence.26. The method of claim 19, wherein the at least one mitochondrialmarker having prognostic value for gastric cancer metastasis andrecurrence comprises at least one of NDUFS5, VDAC3, ATP5O, IMMT, MRPL28,COX5B, MRPL52, and PRKDC.
 27. The method of claim 19, wherein the atleast one mitochondrial marker having prognostic value for gastriccancer metastasis and recurrence comprises at least two of NDUFS5,VDAC3, ATP5O, IMMT, MRPL28, COX5B, MRPL52, and PRKDC.
 28. The method ofclaim 19, wherein the at least one mitochondrial marker havingprognostic value for gastric cancer metastasis and recurrence comprisesthe combination of NDUFSS, VDAC3, ATP5O, IMMT, MRPL28, COX5B, MRPL52,and PRKDC.
 29. A method for identifying a ovarian cancer patient foranti-mitochondrial therapy, the method comprising: obtaining a ovariantumor sample obtained from the patient; determining a level of at leastone mitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence selected from: a prognostic mitochondrial heatshock protein or mRNA comprising HSPA9; at least one prognosticmitochondrial membrane protein or mRNA selected from IMMT, TIMM10,TIMM17A, TIMMIOB, TIMM23, TOMM70A, VDAC2, VDAC3, SLC25A5, and SLC25A32;at least one prognostic mitochondrial antioxidant protein or mRNAselected from NQO1 and SOD2; a prognostic mitochondrial creatine kinasecomprising CKMT2; at least one prognostic mitochondrial large ribosomalsubunit protein or mRNA selected from MRPL49, MRPL34, MRPL35, MRPL23,MRPL18, MRPL48, MRPL17, MRPL16, MRPL11, and MRPL4; at least oneprognostic mitochondrial small ribosomal subunit protein or mRNAselected from MRPS14, MRPS12, MRPS4, MRPS28, MRPS2, MRPS22, MRPS33,MRPS35, MRPS31, and MRPS15; at least one prognostic OXPHOS complex Isubunit protein or mRNA selected from NDUFA3, NDUFB11, NDUFS3, NDUFB2,NDUFB3, NDUFS8, NDUFB2, NDUFB6, NDUFA7, NDUFA13, NDUFS4, NDUFA8, NDUFSS,NDUFV2, NDUFV1, NDUFA2, NDUFS7, NDUFA10, NDUFA1, NDUFA9, and NDUFS2; atleast one prognostic OXPHOS complex II subunit protein or mRNA selectedfrom SDHC and SDHB; at least one prognostic OXPHOS complex III subunitprotein or mRNA selected from UQCRFS1, UQCR7, UQCR6, UQCR, and UQCR2; atleast one prognostic OXPHOS complex IV subunit protein or mRNA selectedfrom COX6B, COX17, COX10, COX5B, COX7B, COX4NB, COX4I1, COX8A, andCOX7A; at least one prognostic OXPHOS complex V subunit protein or mRNAselected from ATP5C, ATP5L, ATP5G, ATP5G3, ATP5J2, PPA1, and ATP5J;classifying the patient as a candidate for therapy with ananti-mitochondrial therapy, wherein a patient is classified as acandidate for therapy with an anti-mitochondrial therapy if the sampleis determined to have an increased level of the at least onemitochondrial marker relative to a threshold level; and if the patientis classified as a candidate for anti-mitochondrial therapy,administering at least one mitochondrial inhibitor.
 30. The method ofclaim 29, wherein the mitochondrial inhibitor inhibits the propagationof ovarian cancer stem cells.
 31. The method of claim 30, wherein theovarian cancer stem cells comprise drug-resistant stem cells, andfurther comprising administering at least one of an OXPHOS inhibitor, aglycolysis inhibitor, and an autophagy inhibitor.
 32. The method ofclaim 29, wherein the at least one mitochondrial inhibitor comprises atleast one mitochondrial biogenesis inhibitor and at least one of anOXPHOS inhibitor, a glycolysis inhibitor, and an autophagy inhibitor.33. The method of claim 29, wherein the mitochondrial inhibitor is atleast one of a mitoriboscin, a mitoketoscin, a antimitoscin, metformin,a tetracycline family member, a erythromycin family member, atovaquone,bedaquiline, vitamin c, caffeic acid phenyl ester, and berberine. 34.The method of claim 29, further comprising determining a level of atleast two mitochondrial marker having prognostic value for ovariancancer metastasis and recurrence.
 35. The method of claim 29, furthercomprising determining a level of at least three mitochondrial markershaving prognostic value for ovarian cancer metastasis and recurrence.36. The method of claim 29, wherein the at least one mitochondrialmarker having prognostic value for ovarian cancer metastasis andrecurrence comprises at least one of UQCRFS1 and MRPL49.
 37. The methodof claim 29, wherein the at least one mitochondrial marker havingprognostic value for ovarian cancer metastasis and recurrence comprisesthe combination of UQCRFS1 and MRPL49.
 38. The method of claim 29,wherein the at least one mitochondrial marker having prognostic valuefor ovarian cancer metastasis and recurrence comprises the combinationof UQCRFS1 and NDUFA3.
 39. The method of claim 38, wherein the at leastone mitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence further comprises PCNA.
 40. A method fortreating breast cancer with an anti-mitochondrial therapy, the methodcomprising: administering at least one mitochondrial inhibitor if abreast cancer sample level of at least one mitochondrial marker havingprognostic value for breast cancer metastasis and recurrence exceeds athreshold level; wherein the at least one mitochondrial marker havingprognostic value for breast cancer metastasis and recurrence comprises:at least one prognostic mitochondrial chaperone protein or mRNA selectedfrom HSPD1, HSPA9, FXN, and TRAP1; at least one prognostic mitochondrialmembrane protein or mRNA selected from VDAC2, AKAP1, IMMT, TOMM70A,TIMM44, TIMM13, TIMM17A, TIMM17A, TIMM17B; at least one prognosticmitochondrial carrier family protein or mRNA selected from SLC25A38,SLC25A1, SLC25A5, SLC25A32; the prognostic mitochondrial antioxidantprotein or mRNA SOD2; at least one prognostic mitochondrial creatinekinase selected from CKMT2 and CKMT1A; at least one prognostic largemitochondrial ribosomal subunit protein or mRNA selected from MRPL15,MRPL18, MRPL46, MRPL24, MRPL13, MRPL48, MRPL3, MRPL23, MRPL4, MRPL17,MRPL42, and MRPL44; at least one prognostic small mitochondrialribosomal subunit protein or mRNA selected from MRPS12, MRPS11, MRPS28,MRPL42, MRPS22, and MRPS33; at least one prognostic OXPHOS complex Isubunit protein or mRNA selected from NDUFA8, NDUFA6, NDUFS1, NDUFS3,NDUFB6, NDUFV1, NDUFS6, and NDUFA1; at least one prognostic OXPHOScomplex III subunit protein or mRNA selected from UQCRB, UQCR6, UQCR4,and UQCRC2; at least one prognostic OXPHOS complex IV subunit protein ormRNA selected from COX17, COXSB, COX4I1, COX6A1, COX4NB, and COX7A2; andat least one OXPHOS complex V subunit selected from ATP5J, ATP5J2,ATP5C1, ATP5C1, ATP5C1, PPA1, ATP5O, ATP5E, and ATP5G3.
 41. The methodof claim 40, wherein the mitochondrial inhibitor inhibits thepropagation of breast cancer stem cells.
 42. The method of claim 41,wherein the breast cancer stem cells comprise drug-resistant stem cells,and further comprising administering at least one of an OXPHOSinhibitor, a glycolysis inhibitor, and an autophagy inhibitor.
 43. Themethod of claim 40, wherein the at least one mitochondrial inhibitorcomprises at least one mitochondrial biogenesis inhibitor and at leastone of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagyinhibitor.
 44. The method of claim 40, wherein the mitochondrialinhibitor is at least one of a mitoriboscin, a mitoketoscin, aantimitoscin, metformin, a tetracycline family member, a erythromycinfamily member, atovaquone, bedaquiline, vitamin c, caffeic acid phenylester, and berberine.
 45. The method of claim 40, wherein the at leastone mitochondrial marker having prognostic value for breast cancermetastasis and recurrence comprises the combination of HSPD1, UQCRB,MRPL15, and COX17.
 46. The method of claim 40, wherein the at least onemitochondrial marker having prognostic value for breast cancermetastasis and recurrence comprises the combination of VDAC2 and HSPD1.47. A method for treating lung cancer with an anti-mitochondrialtherapy, the method comprising: administering at least one mitochondrialinhibitor if a lung cancer sample level of at least one mitochondrialmarker having prognostic value for lung cancer metastasis and recurrenceexceeds a threshold level; wherein the at least one mitochondrial markerhaving prognostic value for lung cancer metastasis and recurrencecomprises: at least one prognostic mitochondrial heat shock protein ormRNA or mitochondrial membrane protein or mRNA selected from HSPD1,TIMM23, TIMM8B, TIMM17B, TIMM44, TIMM10B, TIMM9, TIMM17A, TIMM13,TIMM23, TIMM10, TOMM40, TOMM22, TOMM34, TOMM7, TOMM70A, TOMM20, VDAC1,VDAC3, VDAC2, AKAP1, and SLC25A5; at least one prognostic mitochondrialcreatine kinase selected from CKMT1A and CKMT2; at least one prognosticmitochondrial genome maintenance protein or mRNA selected from PRKDC,PRKDC, and PRKDC; at least one prognostic large mitochondrial ribosomalsubunit protein or mRNA selected from MRPL48, MRPL23, MRPL11, MRPL52,MRPL34, MRPL12, MRPL2, MRPL42, MRPL24, MRPL4, MRPL44, MRPL17, MRPL35,MRPL28, MRPL20, MRPL49, MRPL13, MRPL16, MRPL40, MRPL15, and MRPL33; atleast one prognostic small mitochondrial ribosomal subunit protein ormRNA selected from MRPS12, MRPS12, MRPS12, MRPS12, MRPS7, MRPS2, MRPS4,MRPS11, MRPS34, MRPS31, MRPS28, MRPS35, MRPS15, MRPS27, MRPS30, MRPS33,and MRPS14; at least one prognostic OXPHOS complex I subunit protein ormRNA selected from NDUFB3, NDUFS8, NDUFS8, NDUFS4, NDUFA4L2, NDUFB4,NDUFA13, NDUFV2, NDUFS3, NDUFA10, NDUFA3, NDUFB8, NDUFB2, NDUFA5,NDUFA7, NDUFA1, NDUFS2, NDUFB7, NDUFS5, NDUFA2, NDUFA9, NDUFS7, NDUFB6,NDUFA2, NDUFB11, NDUFB2, and NDUFV1; at least one prognostic OXPHOScomplex II subunit protein or mRNA selected from SDHC and SDHB; at leastone prognostic OXPHOS complex III subunit protein or mRNA selected fromUQCR7, UQCR6, UQCR8, UQCRFS1, UQCR4/CYC1, BCS1L, and UQCR; at least oneprognostic OXPHOS complex IV subunit protein or mRNA selected fromCOX5B, COX6A, COX8A, COX17, COX6C, COX7A2, COX6B, COX6A2, COX10, COX7B,COX10, COX15, COX5A, COX4NB, COX7A, and COX4I1; at least one prognosticOXPHOS complex V subunit protein or mRNA selected from ATP5J2, ATP5G3,ATP5H, ATP5I, ATP5D, ATP5G2, ATP5E, ATP5L, ATP5B, ATP5S, ATP5G, ATP5O,and ATP5C.
 48. The method of claim 47, wherein the mitochondrialinhibitor inhibits the propagation of lung cancer stem cells.
 49. Themethod of claim 48, wherein the lung cancer stem cells comprisedrug-resistant stem cells, and further comprising administering at leastone of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagyinhibitor.
 50. The method of claim 47, wherein the at least onemitochondrial inhibitor comprises at least one mitochondrial biogenesisinhibitor and at least one of an OXPHOS inhibitor, a glycolysisinhibitor, and an autophagy inhibitor.
 51. The method of claim 47,wherein the mitochondrial inhibitor is at least one of a mitoriboscin, amitoketoscin, a antimitoscin, metformin, a tetracycline family member, aerythromycin family member, atovaquone, bedaquiline, vitamin c, caffeicacid phenyl ester, and berberine.
 52. A method for treating gastriccancer with an anti-mitochondrial therapy, the method comprising:administering at least one mitochondrial inhibitor if a gastric cancersample level of at least one mitochondrial marker having prognosticvalue for gastric cancer metastasis and recurrence exceeds a thresholdlevel; wherein the at least one mitochondrial marker having prognosticvalue for gastric cancer metastasis and recurrence comprises: at leastone prognostic heat shock protein or mRNA or mitochondrial chaperoneprotein or mRNA selected from HSPD1, HSPA9, and FXN; at least oneprognostic mitochondrial membrane protein or mRNA selected from VDAC3,VDAC2, IMMT, TIMM23, TIMM10, TIMM8B, TIMMI7A, TOMM34, and TOMM40; aprognostic mitochondrial antioxidant protein or mRNA comprising SOD2; aprognostic mitochondrial genome maintenance protein or mRNA comprisingPRKDC; at least one prognostic large mitochondrial ribosomal subunitprotein or mRNA selected from MRPL28, MRPL52, MRPL17, MRPL20, MRPL18,MRPL2, MRPL12, MRPL3, MRPL42, MRPL13, MRPL48, and MRPL23; at least oneprognostic small mitochondrial ribosomal subunit protein or mRNAselected from MRPS11, MRPS12, MRPS14, MRPS22, MRPS28, and MRPS34; atleast one prognostic OXPHOS complex I subunit protein or mRNA selectedfrom NDUFS5, NDUFA5, NDUFA9, NDUFS6, NDUFB8, NDUFB3, NDUFB4, NDUFA6,NDUFA8, NDUFA7, and NDUFA3; a prognostic OXPHOS complex H subunitprotein or mRNA comprising SDHB; at least one prognostic OXPHOS complexIII subunit protein or mRNA selected from BCS1L and UQCR8; at least oneprognostic OXPHOS complex IV subunit protein or mRNA selected fromCOX5B, COX4NB, COX6C, COX6B1, COX6A1, COX17, COXSA, COX7B, COX7A2, andCOX10; and at least one prognostic OXPHOS complex V subunit protein ormRNA selected from ATP5O, ATP5G2, ATP5I, ATP5E, ATP5G1, ATP5H, ATP5J2,ATP5L, ATP5C, ATP5S, and ATP5C1.
 53. The method of claim 52, wherein themitochondrial inhibitor inhibits the propagation of gastric cancer stemcells.
 54. The method of claim 53, wherein the gastric cancer stem cellscomprise drug-resistant stem cells, and further comprising administeringat least one of an OXPHOS inhibitor, a glycolysis inhibitor, and anautophagy inhibitor.
 55. The method of claim 52 wherein the at least onemitochondrial inhibitor comprises at least one mitochondrial biogenesisinhibitor and at least one of an OXPHOS inhibitor, a glycolysisinhibitor, and an autophagy inhibitor.
 56. The method of claim 52,wherein the mitochondrial inhibitor is at least one of a mitoriboscin, amitoketoscin, a antimitoscin, metformin, a tetracycline family member, aerythromycin family member, atovaquone, bedaquiline, vitamin c, caffeicacid phenyl ester, and berberine.
 57. The method of claim 52, whereinthe at least one mitochondrial marker having prognostic value forgastric cancer metastasis and recurrence comprises at least two or moreof NDUFS5, VDAC3, ATPSO, IMMT, MRPL28, COXSB, MRPL52, and PRKDC.
 58. Amethod for treating ovarian cancer with an anti-mitochondrial therapy,the method comprising: administering at least one mitochondrialinhibitor if a ovarian cancer sample level of at least one mitochondrialmarker having prognostic value for ovarian cancer metastasis andrecurrence exceeds a threshold level; wherein the at least onemitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence comprises: a prognostic mitochondrial heatshock protein or mRNA comprising HSPA9; at least one prognosticmitochondrial membrane protein or mRNA selected from IMMT, TIMM10,TIMM17A, TIMM10B, TIMM23, TOMM70A, VDAC2, VDAC3, SLC25A5, and SLC25A32;at least one prognostic mitochondrial antioxidant protein or mRNAselected from NQO1 and SOD2; a prognostic mitochondrial creatine kinasecomprising CKMT2; at least one prognostic mitochondrial large ribosomalsubunit protein or mRNA selected from MRPL49, MRPL34, MRPL35, MRPL23,MRPL18, MRPL48, MRPL17, MRPL16, MRPL11, and MRPL4; at least oneprognostic mitochondrial small ribosomal subunit protein or mRNAselected from MRPS14, MRPS12, MRPS4, MRPS28, MRPS2, MRPS22, MRPS33,MRPS35, MRPS31, and MRPS15; at least one prognostic OXPHOS complex Isubunit protein or mRNA selected from NDUFA3, NDUFB11, NDUFS3, NDUFB2,NDUFB3, NDUFS8, NDUFB2, NDUFB6, NDUFA7, NDUFA13, NDUFS4, NDUFA8, NDUFS8,NDUFV2, NDUFV1, NDUFA2, NDUFS7, NDUFA10, NDUFA1, NDUFA9, and NDUFS2; atleast one prognostic OXPHOS complex II subunit protein or mRNA selectedfrom SDHC and SDHB; at least one prognostic OXPHOS complex III subunitprotein or mRNA selected from UQCRFS1, UQCR7, UQCR6, UQCR, and UQCR2; atleast one prognostic OXPHOS complex IV subunit protein or mRNA selectedfrom COX6B, COX17, COX10, COX5B, COX7B, COX4NB, COX4I1, COX8A, andCOX7A; and at least one prognostic OXPHOS complex V subunit protein ormRNA selected from ATP5C, ATP5L, ATP5G, ATP5G3, ATP5J2, PPA1, and ATP5J.59. The method of claim 58, wherein the mitochondrial inhibitor inhibitsthe propagation of ovarian cancer stem cells.
 60. The method of claim59, wherein the ovarian cancer stem cells comprise drug-resistant stemcells, and further comprising administering at least one of an OXPHOSinhibitor, a glycolysis inhibitor, and an autophagy inhibitor.
 61. Themethod of claim 58, wherein the at least one mitochondrial inhibitorcomprises at least one mitochondrial biogenesis inhibitor and at leastone of an OXPHOS inhibitor, a glycolysis inhibitor, and an autophagyinhibitor.
 62. The method of claim 58, wherein the mitochondrialinhibitor is at least one of a mitoriboscin, a mitoketoscin, aantimitoscin, metformin, a tetracycline family member, a erythromycinfamily member, atovaquone, bedaquiline, vitamin c, caffeic acid phenylester, and berberine.
 63. The method of claim 58, wherein the at leastone mitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence comprises the combination of UQCRFS1 andMRPL49.
 64. The method of claim 58, wherein the at least onemitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence comprises the combination of UQCRFS1 andNDUFA3.
 65. The method of claim 67, wherein the at least onemitochondrial marker having prognostic value for ovarian cancermetastasis and recurrence further comprises PCNA.